snprelate_ld: Wrapper for snpgdsLDMat to compute r2

In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Wrapper for snpgdsLDMat to compute r2

Description

Wrapper for snpgdsLDMat to compute r2

Usage

snprelate_ld(
  gdata,
  window_size = 0,
  min_r2 = 0,
  snps_idx = NULL,
  scans_idx = NULL,
  threads = 1,
  quiet = FALSE
)

Arguments

gdata	A GenotypeData object
window_size	Max number of SNPs in LD window, 0 for no window
min_r2	Minimum r2 value to report
snps_idx	Indices of snps to use
scans_idx	Indices of scans to use
threads	The number of threads to use
quiet	Whether to be quiet

Value

A data frame with columns SNP_A, SNP_B, R2 for r2 >= min_r2

snplinkage documentation built on May 4, 2023, 9:09 a.m.